def extract_data_from_tar_file(tar_file):
with tarfile.open(tar_file, 'r:gz') as tar:
tar.extractall()
folder = tar_file.replace('.tar.gz', '')
with cd(folder):
tdout = GaussianOutput('td.log')
td_exit = tdout.read_excitation_energies()
td_triplet = [e for e in td_exit if 'triplet' in e[3].lower()][0][0]
td_singlet = [e for e in td_exit if 'singlet' in e[3].lower()][0][0]
tdaout = GaussianOutput('tda.log')
tda_exit = tdaout.read_excitation_energies()
tda_triplet = [e for e in tda_exit if 'triplet' in e[3].lower()][0][0]
tda_singlet = [e for e in tda_exit if 'singlet' in e[3].lower()][0][0]
nicssout = GaussianOutput('nics_singlet.log')
# occasionally some jobs fail here
if not nicssout.properly_terminated:
return False
nicss_mag = nicssout.read_magnetic_shielding()
nicss_six_ring_above = (abs(nicss_mag[-8]['isotropic']) +
abs(nicss_mag[-6]['isotropic']))/2
nicss_six_ring_below = (abs(nicss_mag[-7]['isotropic']) +
abs(nicss_mag[-5]['isotropic']))/2
nicss_five_ring_above = (abs(nicss_mag[-4]['isotropic']) +
abs(nicss_mag[-2]['isotropic']))/2
nicss_five_ring_below = (abs(nicss_mag[-3]['isotropic']) +
abs(nicss_mag[-1]['isotropic']))/2
nicstout = GaussianOutput('nics_triplet.log')
if not nicstout.properly_terminated:
return False
nicst_mag = nicstout.read_magnetic_shielding()
nicst_six_ring_above = (abs(nicst_mag[-8]['isotropic']) +
abs(nicst_mag[-6]['isotropic']))/2
nicst_six_ring_below = (abs(nicst_mag[-7]['isotropic']) +
abs(nicst_mag[-5]['isotropic']))/2
nicst_five_ring_above = (abs(nicst_mag[-4]['isotropic']) +
abs(nicst_mag[-2]['isotropic']))/2
nicst_five_ring_below = (abs(nicst_mag[-3]['isotropic']) +
abs(nicst_mag[-1]['isotropic']))/2
data = {'td_singlet': td_singlet, 'td_triplet': td_triplet,
'tda_singlet': tda_singlet, 'tda_triplet': tda_triplet,
'nicss_six_ring_above': nicss_six_ring_above,
'nicss_six_ring_below': nicss_six_ring_below,
'nicss_five_ring_above': nicss_five_ring_above,
'nicss_five_ring_below': nicss_five_ring_below,
'nicst_six_ring_above': nicst_six_ring_above,
'nicst_six_ring_below': nicst_six_ring_below,
'nicst_five_ring_above': nicst_five_ring_above,
'nicst_five_ring_below': nicst_five_ring_below}
return data
def make_json(mol_dir, mol_name, json_file):
"""
For a molecule directory, mol_dir, this finds the molecule name, frequencies
value, and runtiime and places those into json_file.
"""
log_files = [x for x in os.listdir(mol_dir) if x.endswith('.log')]
if len(log_files) > 0:
log_fn = log_files[0]
log_path = os.path.join(mol_dir, log_fn)
mol = GaussianOutput(log_path)
runtime = runtime_from_log(log_path)
if mol.properly_terminated:
charge = mol.charge
try:
excitations = mol.read_excitation_energies()
except IndexError:
excitations = None
# Write json
json_data = {"molecule_name": mol_name, "excitations": excitations, "charge": charge, "runtime": runtime}
write_json(json_data, json_file)
print("Data collected for {}".format(mol_name))
else:
print("Error. Calculation did not properly terminate for {}".format(mol_name))
else:
print("No log file for ", mol_name)
def test_td(self):
gau = GaussianOutput(os.path.join(test_dir, "so2_td.log"))
transitions = gau.read_excitation_energies()
self.assertEqual(len(transitions), 4)
self.assertAlmostEqual(transitions[0], (3.9281, 315.64, 0.0054))
def test_td(self):
gau = GaussianOutput(os.path.join(test_dir, "so2_td.log"))
transitions = gau.read_excitation_energies()
self.assertEqual(len(transitions), 4)
self.assertAlmostEqual(transitions[0], (3.9281, 315.64, 0.0054))